Genotype F of Echovirus 25 with multiple recombination pattern have been persistently and extensively circulating in Chinese mainland

Abstract

Echovirus 25 (E25), a member of the Enterovirus B (EV-B) species, can cause aseptic meningitis (AM), viral meningitis (VM), and acute flaccid paralysis (AFP). However, systematic studies on the molecular epidemiology of E25, especially those concerning its evolution and recombination, are lacking. In this study, 18 strains of E25, isolated from seven provinces of China between 2009 and 2018, were collected based on the Chinese hand, foot, and mouth disease (HFMD) surveillance network, and 95 sequences downloaded from GenBank were also screened. Based on the phylogenetic analysis of 113 full-length VP1 sequences worldwide, globally occurring E25 strains were classified into 9 genotypes (A-I), and genotype F was the dominant genotype in the Chinese mainland. The average nucleotide substitution rate of E25 was 6.08 × 10^-3 substitutions/site/year, and six important transmission routes were identified worldwide. Seventeen recombination patterns were determined, of which genotype F can be divided into 9 recombination patterns. A positive selector site was found in the capsid protein region of genotype F. Recombination analysis and pressure selection analysis for genotype F showed multiple recombination patterns and evolution characteristics, which may be responsible for it being the dominant genotype in the Chinese mainland. This study provides a theoretical basis for the subsequent prevention and control of E25.

Figure 1

The maximum likelihood phylogenetic tree is based on the entire VP1 genome of 113 E25 genome sequences. Filled circle: ⚫E25 strains in this study. Filled rhombus: ◆E25 prototype strain.

Figure 2

(A)The maximum clade credibility (MCC) phylogenetic tree was generated using the Markov chain Monte Carlo (MCMC) method based on 110 complete VP1 sequences of E25. The color of the branches represents the isolates of different genotypes. (B) Bayesian skyline plot of the whole E25 VP1 region sequence, reflecting the relative genetic diversity of E25 from 1957 to 2018. The X-axis is the time scale (year), and the Y-axis is the effective population size; the solid line is the estimated median, and the blue shadow is the 95% highest posterior density. (C) Bayesian skyline plot of theVP1 region sequence of E25 Genotype F.

Figure 3

(A) The global spatial transmission route of E25. (B) The histogram of the average number of state transitions is based on the geographical location of six countries.

Figure 4

NJ trees based on P1, P2, and P3 regions of the prototype sequence of all Enteroviruses B in the GenBank database with 37 E25 strains. Filled rhombus: indicates E25 prototype strain (JV-4), filled circle: E25 strains in this study. Numbers on codes indicate the bootstrap support of the node (1000 bootstrap replicate percentage). (A) P1 coding sequences; (B) P2 coding sequences; (C) P3 coding sequences. (D) Recombination breakpoints based on the whole genomes of different lineages as detected within genotypes. (E) Genomic mapping of representative strain recombination events predicted using RDP4 software for E25.

Figure 5

Positive amino acid selector sites in the VP1 region of E25. Positive selector sites are located at the blue square markers.